The Philippines is seeking compensation for damage to a protected marine area where a Vietnamese cargo ship has run aground and damaged coral reef.

The vessel MV Ocean 3, with 21 Vietnamese crew, was departing the central port of Legazpi city after unloading its rice cargo, when it ran aground on a three-hectare marine protected area known as Denson Reef or Pulang Buya.

Coastal officials in Legazpi are demanding a payment of almost $US100,000 from the owner of the Vietnamese cargo vessel to rehabilitate an estimated 1000 square metres of coral reef and to compensate local fishermen.

A fishing ban may be imposed during rehabilitation which could affect the livelihood of Legazpi fishermen, who are allowed to use the marine conservation area for traditional hook-and-line fishing.

Scientists found crushed corals and giant clams tainted with paint believed to have come from the hull of the ship.